CN103997404B - A kind of DNA self-assembled structures and the symmetric encryption system based on it - Google Patents
A kind of DNA self-assembled structures and the symmetric encryption system based on it Download PDFInfo
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Abstract
The present invention relates to a kind of DNA self-assembled structures and the symmetric encryption system based on it, the DNA self-assembled structures include balloon-shaped structure, formed by DNA nanostructure with chain Q by base pairing, wherein DNA nanostructure is hybridized with chain BHQ chains by DNA AB and formed, by the huge parallel abilities of DNA, large-scale information search and single molecular recognition ability, with possess in complex biological body using different detection methods to complete the conversion of information, transmission and the inherent advantage of detection, and the difficulty based on nanometer technology in extensive information search, utilize DNA self-assembled structures, realize and encrypted in stream encryption method and decrypt；Specific recognition region and strand displacement technology of the symmetric encryption system by AB chains, realize XOR, complete the information encryption of one-time pad and decrypt, so as to ensure being difficult to cracking and improving the security of information Store and transmission for password.A kind of DNA self-assembled structures and the symmetric encryption system based on it can be widely used in each password field.
Description
Technical field
The present invention relates to cryptography research field, more particularly to DNA passwords field.
Background technology
Contemporary cryptology is based on a variety of difficult difficult math questions such as nonpolynomial time complete problem (NP-C).Quantum
Cryptography is then the physics problem based on Heisenberg's uncertainty principle (Heisenberg uncertain principle).
Contemporary cryptology and quantum cryptology lack huge parallel ability, large-scale information search, for the encryption of bulk information,
Speed is slower, and the ciphertext of these passwords is easily intercepted and captured by attacker, may be cracked.In addition conventional encryption methods
Dependent on difficult mathematical problem, and these problems are once solved encryption method will be made to fail.
In recent years, the advantages such as the huge parallelism and high density data storage that have due to DNA molecular, it is extensive
In terms of calculating, data storage, cryptography.One new direction of DNA passwords --- cryptography research field, is several
, information science, nanometer technology and the multi-disciplinary cross products of molecular biology.
DNA passwords are due to concern of the superpower information storage capability by scholars, and gradually from theory hair
Open up application.1999,《It is natural》A kind of Novel DNA " Steganography " is reported on periodical, it contains one by what PCR was obtained
The short chain DNA of section coding information is encrypted and decrypted to realize.From that time, the research in DNA passwords field causes extensive pass
Note.With the development of correlation technique, many nanometer technologies have also been increasingly used for DNA cryptosystems, such as DNA hybridization, DNA
Self assembly and strand displacement, DNA chip and DNA/ nano particle combinations etc..
To sum up state, how by parallel ability huge DNA, large-scale information search and single molecular recognition ability, and
Possess in complex biological body in the conversion, transmission and detection using different detection methods to complete information in advantage, and
Difficulty based on nanometer technology in extensive information search, proposes a kind of new DNA self-assembled structures；And being based on should
DNA self-assembled structures provide a kind of symmetric encryption system, so that the encryption and decryption of stream encryption method in DNA cryptosystems are realized,
Ensure password is difficult to cracking and raising information Store and the security of transmission, is a great problem of the prior art.
The content of the invention
(1) technical problem to be solved
The technical problem to be solved in the present invention be how by DNA password field advantage there is provided a kind of DNA from group
Assembling structure and the symmetric encryption system based on it, so as to realize the encryption and decryption of stream encryption method in DNA cryptosystems.
(2) technical scheme
In order to solve the above-mentioned technical problem, the invention provides a kind of DNA self-assembled structures, the DNA self-assembled structures
Including balloon-shaped structure, by DNA nanostructure and chain Q, formed by base pairing, wherein DNA nanostructure is by DNA AB and chain
BHQ chains hybridize to be formed.
Wherein, chain Q includes three sections of sequences, in being respectively head end sequence Q1, end sequence Q2 and intermediate sequence Q3, chain Q
Between sequence Q3 modified by fluorescent base Cy3, a part of sequence of head end sequence Q1 chains and AB chains is complementary, end sequence Q2 and AB chains
Another part sequence is complementary, and the 3 ' ends of the BHQ are marked by fluorescent quenching base BHQ, and it completely with AB middle-of-chain sequences
Complementation, now Q3 be quenched by the fluorescent quenching base at the BHQ of near-end 3 ' ends, when Q chains are replaced and during with AB chain separations, fluorescence
Intensity, which will be with fluorescent base and the separation of quencher, correspondingly to be increased.
The present invention also provides a kind of symmetric encryption system, it is characterised in that the symmetric encryption system includes described DNA
Self-assembled structures, and including XOR operating system.
The present invention also provides a kind of symmetric encryption method according to described symmetric encryption system, it is characterised in that including
Following steps：
Step one：Definition DNA sequential coding, in xor operation, M represents that in plain text, S represents key, and C is ciphertext or fluorescence
Signal, plaintext M, ciphertext or fluorescence signal C and key S respectively with AB chain part regional complementarities, plaintext M, ciphertext or fluorescence signal C
Binary string is changed into key S；
Step 2：Encryption, the DNA self-assembled structures of structure encrypt key S and the DNA of plaintext M as initial computing module
Chain, carries out strand replacement reaction with initial computing module and implements logic XOR, ciphertext or fluorescence signal C are obtained, so as to complete
The DNA ciphering process of plaintext M；
Step 3：Decryption, decruption key S and ciphertext or fluorescence signal C DNA, carry out chain with DNA self-assembled structures and put
Change reaction and implement logic XOR, so as to complete ciphertext or fluorescence signal C DNA decrypting processes；
Wherein, the xor operation of each of plaintext M is completed in single test tube.
Preferably, in encryption and decryption processes, the AB chains of DNA self-assembled structures are AB1 chains and AB2 chains respectively, AB1 chains and
The specific recognition region of AB2 chains is different, and encryption key is different with the DNA sequence dna of decruption key.
Preferably, when realizing the encryption of information to plaintext M execution xor operation, produce fluorescence signal and represent " 1 ", do not produce
Raw fluorescence signal represents " 0 ", and the fluorescence signal of all connects together expression ciphertext, is then transferred to recipient.
(3) beneficial effect
The DNA self-assembled structures of the present invention and the symmetric encryption system based on it, by parallel ability huge DNA, greatly
The information search of scale and single molecular recognition ability, and possess in complex biological body using different detection methods to complete information
Conversion, transmission and detection inherent advantage, and the difficulty based on nanometer technology in extensive information search utilizes
DNA self-assembled structures, realize and encrypted in stream encryption method and decrypt.By specific recognition region and strand displacement technology, realize different
Or computing, complete one-time pad information encryption and decrypt so that ensure password be difficult to cracking and improve information Store
With the security of transmission.
Brief description of the drawings
In order to illustrate more clearly about the embodiment of the present invention or technical scheme of the prior art, below will be to embodiment or existing
The accompanying drawing to be used needed for having technology description is briefly described, it should be apparent that, drawings in the following description are only this
Some embodiments of invention, for those of ordinary skill in the art, on the premise of not paying creative work, can be with
Other accompanying drawings are obtained according to these accompanying drawings.
Fig. 1：A kind of DNA self-assembled structures forming process schematic diagram that the present invention is provided；
Fig. 2：The system process figure for the symmetric encryption system that the present invention is provided；
Fig. 3：The process schematic that XOR is carried out using strand displacement for the symmetric encryption system that the present invention is provided；
Fig. 4：Fluorescence intensity level of the wavelength for the symmetric encryption system that the present invention is provided in 564nm, wherein L1-L3 difference
Represent single input A1 chains, single input B1 chains, dual input A1 and B1 chain；
Fig. 5：The XOR XOR logical operation electrophoresis detection result for the symmetric encryption system that the present invention is provided；
Fig. 6：The encryption fluoroscopic examination result for the symmetric encryption system that the present invention is provided；
Fig. 7：The decryption fluoroscopic examination result for the symmetric encryption system that the present invention is provided；
Embodiment
Embodiments of the present invention are described in further detail with reference to the accompanying drawings and examples.Following examples are used for
Illustrate the present invention, but can not be used for limiting the scope of the present invention.
Embodiment 1：The formation basic procedure of DNA self-assembled structures is as shown in Figure 1.
Based on DNA self-assembled structures, a kind of symmetric encryption system is constructed.The encryption key that sender uses is named as
Ka.Plaintext P is converted to ciphertext C by sender with Ka, and this ciphertext is sent into a recipient, and recipient possesses decruption key
Kb.Receive after ciphertext C, recipient obtains plaintext P by decrypting process with Kb.This AES uses one-time pad
XOR.And xor operation is the gate of an execution XOR, that is, when only one input is true (1)
Output result is true (1), if it is that output result is false (0) when true (1) or input are false (0) to fully enter.
" code " is selected in the present invention to be encrypted and decrypted as in plain text.According to ASCII passwords, this can turn in plain text
Turn to binary string " 01,100,011 01,101,111 0110010001100101 ".Assuming that key is by binary string " 10001111
10011100 1110011101101011 " represent.Specific calculation procedure such as Fig. 2 of DNA cryptographic systems, comprises the following steps：
The first step：Definition DNA sequential coding, as shown in figure 1, for constructed dna self-assembled structures, several different DNA
Chain (AB1, BHQ and Q) is designed and synthesized, and length is 74bp, 14bp, and 53bp respectively.In order to perform encryption and decrypt, respectively
With the DNA A1 and B1 of AB1 chain part regional complementarities, plaintext or key are used as in xor operation.M represents that in plain text, S represents close
Key, C is ciphertext or fluorescence signal.Whether M or S, A1 chain represent input data " 1 ", and B1 chains represent input data " 0 ".It is real
Test the middle all DNAs used and be shown in Table 1：
Table 1
Second step：Encryption, using DNA self-assembled structures, the encryption that xor operation realizes information, such as Fig. 3 are performed to plaintext M
It is shown.Because the xor operation of each is completed in single test tube, therefore all bit manipulations of plaintext are all parallel
's.Produce fluorescence signal and represent " 1 ", do not represent " 0 ".The fluorescence signal of so all connects together expression ciphertext, then
Send recipient to.If without decruption key, it be extremely difficult in plain text directly to be read from DNA self-assembled structures, this be because
Caused by the variation of DNA sequence dna.
3rd step：Decryption, recipient reads ciphertext with decruption key.It is similar with encryption key, the DNA of decruption key with
The Sequence of AB2 chains is complementary, and AB2 chains are different from the specific recognition region of AB1 chains.By xor operation, ciphertext can turn
It is changed in plain text.Decrypting process is identical with ciphering process, and result of calculation is obtained by fluorescence signal.It is worth noting that, encryption key
DNA sequence dna with decruption key is different.
Embodiment 2：DNA self-assembled structures are formed by the single-stranded hybridization of several different oligonucleotides, and specific method is as follows
It is described：First, by complementarity determining regions domain, single-stranded AB and BHQ hybridize to form a new DNA, in the process, by etc. rub
Your the single-stranded AB and BHQ of concentration are added in system (final concentration 3.75pmol/L, TAE/Mg2+ buffer solution), and mixed liquor is existed
37 DEG C are placed 2 hours.Secondly, Q chains are added in mixed liquor with equimolar concentration, 37 DEG C are placed 2 hours.In experiment, to carry out
The strand replacement reaction of XOR, the mixed liquor containing DNA self-assemblies is added to by input chain (final concentration 3.75pmol/L)
In, react more than 2 hours at room temperature, you can carry out PAGE electrophoresis and fluorescence results detection.For each sample, examined using fluorescence
Instrument is surveyed, the fluorescent value exported at wavelength 564nm is recorded, as shown in Figure 4.
DNA used in experiment gives birth to work purchased from Shanghai, all by PAGE Purified in electrophoresis.
DNA molecular sequence in experiment is shown in Table 1.
The reagent used in experiment is as follows：The double propylene of Na2EDTA, Tris alkali, ammonium persulfate, acrylamide, methylene
Acid amides, tetramethylethylenediamine (TEMED) and Stain all are purchased from Sigma companies.TAE/Mg2+ buffers are as follows：
0.04mol/L Tris alkali, 1mmol/L Na2EDTA, 12.5mmol/L magnesium acetates, adjustment pH is 8.3.Acrylamide mother liquor is matched somebody with somebody
System is as follows：500mL is prepared, concentration is 45% acrylamide mother liquor, weighs 217g acrylamides and 8g methylene bisacrylamides,
Dissolved at 37 DEG C, add deionized water and be settled to 500mL.All DNAs used pass through TU-1901 light splitting light in experiment
Degree meter (being purchased from Beijing Pu Xi all purpose instruments Co., Ltd) carries out concentration mensuration, records every kind of DNA and is absorbed at λ=260nm
Intensity level.Using F-2700 Fluorescence spectrophotometers (Hitachi), the fluorescence that output result is produced is detected, maximum is inhaled
Receipts wavelength is 550nm, and maximum emission wavelength is 564nm.
In this experiment, we are utilized respectively two methods of PAGE electrophoresis and fluorescence signal detection result of calculation.Due to input
Strand displacement occurs for signal and DNA self-assemblies, and the DNA package assemblies of generation change, then electrophoretic velocity in gel also with
Change, therefore result of calculation is readily observed by PAGE electrophoresis.In addition, accuracy and simplicity in order to improve calculating
Property, text in introduce fluorescence signal detection technique, whether there is by fluorescence signal, judge output result.
In cryptographic calculation, the DNA self-assembled structures of structure are as initial computing module, by inputting chain and initial module
Carry out strand replacement reaction and implement logic XOR, so as to complete DNA ciphering process.Here, respectively with first, second,
Exemplified by the information of the 4th and the 7th, cryptographic calculation process is discussed in detail.(1) due to first character point in plain text with key
It is not 0 and 1, therefore represents 0 and 1 DNA sequence dna B1 and A1 while being added in the solution containing DNA self-assembled structures.First,
Recognized by the specific regions on AB chains, input chain A1 and B1 gradually replace Q chains；Then, in order to reach most stable state, A1, B1
A stable double chain DNA molecule is ultimately formed with AB chains, Q chains are released, so that fluorescent base separates generation with base is quenched
Fluorescence signal, as shown in L3 in Fig. 4.(2) the second character in plain text with key is 1 and 0 respectively, therefore represents 1 and 0 DNA
Chain A1 and B1 is added in the solution containing DNA self-assembled structures simultaneously.Identical with primary displacement reaction, Q chains are released,
Fluorescence signal is detected, as shown in L3 in Fig. 4.(3) it is in plain text 0 and 0 respectively with key, so two for the 4th character
Bar represents 0 DNA B1 as input chain, is added in the solution containing DNA self-assembled structures.The 3rd section of Q chains with B1 chains
Specific position be mutually distinguishable and combine, gradually form stable duplex structure.Due to Q chains the 1st section of sequence still with from group
Assembling structure is combined, and Q chains are not released (i.e. fluorescent base is not separated with base is quenched) completely, therefore is produced without fluorescence signal,
As shown in L2 in Fig. 4.In other words, the DNA of expression 0 is only added, it is impossible to produce fluorescence signal.(4) it is bright for the 7th character
Text and key are 1 and 1 respectively, so two represent 1 DNA A1 as input chain, are added to containing DNA self-assembled structures
In solution.The 1st section of Q chains is mutually distinguishable and combined with the specific position on A1 chains, gradually forms stable duplex structure.With
4th calculating is similar, because Q chains are not released completely, therefore is also produced without fluorescence signal, as shown in L1 in Fig. 4.Profit
In this way, final character in plain text on each is all simultaneously parallel in different test tubes carries out cryptographic calculation, by glimmering
Light is detected, obtains one group of fluorescence signal for containing 32.
Output result is 1, is 0 in 1000 following presentation output results.(a) original state when without input signal；(b) add
Fluorescence intensity level when entering to input chain A1, i.e. input signal for (1,1)；(c) it is (0,0) to add input chain B1, i.e. input signal
When fluorescence intensity level；(d) fluorescence intensity level when input chain A1 and B1, i.e. input signal are (1,0) is added；(e) add defeated
Fluorescence intensity level when entering chain B1 and A1, i.e. input signal for (0,1).
On the basis of fluoroscopic examination, experiment further verifies result of calculation using PAGE gel electrophoresises.In order that electrophoresis knot
It is really high-visible, AB long-chains are designed to two short chains A and B.This two short chains and Q chains hybridize to form DNA self-assembled structures.With
The structure is separately added into different input chains as initial module, by strand replacement reaction, produces output chain.Utilize PAGE electricity
Swimming detection, finally gives the result of calculation of XOR.Below electrophoresis detection is carried out by the first and second of plaintext, exemplified by four, seven
Illustrate, as shown in figure 5, swimming lane 1~3,7~9 shows the electrophoretic band of each different self-assembly, swimming lane 4~6 shows different
Or the result of calculation of computing.Result of calculation can carry out interpretation from electrophoretic band position, and (mark position is marked with Chinese red arrow
Represent single-stranded Q electrophoresis position).In XOR calculating, point four kinds of situations are inputted：(0,0), (1,1), (0,1) and
(1,0).(1) when input signal is 1 (chain A1), Q chains are not released completely, and output signal is 0.Swimming lane 4 can from Fig. 5
See, compared to initial configuration swimming lane 3, generate two new bands, be A and the double-strand of A1 chains formation, initial configuration release A respectively
Structure after chain.(2) when input signal is 0 (chain B1), Q chains are not also released completely, and output signal is also 0.Swimming lane 5
Show that with initial configuration the band produced after strand displacement occurs for B1 chains, be B and the double-strand of B1 chains formation respectively, initial configuration is released
Put the structure after B chains.(3) when it is 1 to have one in two input signals (chain B1 and A1), initial configuration disintegrates completely, and Q chains are complete
It is released entirely, output signal is 1.Swimming lane 6 shows that the band produced after strand displacement occurs for chain A1, B1 and initial configuration.Pass through
Compared with swimming lane 7~9, it is found that its position is suitable with Q chains, and also have A and A1 chains, the double-strand of B and B1 chains formation simultaneously.Due to position
Put close, some coincidences of this three band.Detected by electrophoresis result, all experimental results match with fluorescence results.
According to above-mentioned fluorescence detection method, XOR is carried out simultaneously to the character in plain text on each, one is finally obtained
Group is containing the fluorescence signal of 32, as shown in Figure 6.According to the presence or absence of fluorescence signal, obtain one group of new two for representing ciphertext and enter
Character string " 11,101,100 1,111,001,110,000,011 00001110 " processed.Then ciphertext is sent to by disclosed approach and connect
Receipts person Bob, without worrying that encryption information is decrypted, because only that recipient just possesses DNA sequence dna and the self assembly of decruption key
With the reaction condition of strand displacement.
In decryption system, calculation step is identical with encrypting step.Different places is the initial package assemblies of DNA by single-stranded
Q, BHQ and AB2 composition.It is different from the specific recognition regional sequence of AB1 chains, therefore represents the sequence of 1 and 0 decruption key
Row are different from the sequence of encryption key.After recipient receives ciphertext, with the self-assembled structures and decruption key built to close
Text carries out XOR.Eventually through fluoroscopic examination, a string of fluorescence signals are obtained, as shown in fig. 7, and being transcribed into plaintext
String of binary characters.According to the ASCII character table of comparisons, obtain in plain text " code ".
Compared with conventional cipher system, DNA passwords have following two aspects advantage：(1) peace of the DNA passwords than conventional cipher
Quan Xinggao.DNA passwords have two layers of security：First layer security is that the limitation of biotechnology is provided, second layer safety
Property rely on difficult computational problem.On the one hand, DNA self-assembled structures are by controlling to adjust the single-stranded concentration of DNA and reaction condition
Formed etc. factor.Information is encrypted and decryption is to utilize the structure, is completed by DNA strand displacements technology.Therefore, do not obtain
This self-assembled structures, without specific strand replacement reaction condition, even if attacker has obtained decruption key, DNA passwords are not yet
It may be decrypted.On the other hand, coding techniques provides second layer security.Herein, it is easy to operate and realizes to test,
The DNA self-assembled structures used all are the DNA sequence dnas of identical, i.e. key when carrying out computing to each of string of binary characters
It is identical.In order to improve the security of DNA passwords, different DNA self assembly knots can be designed each in the research of next step
Structure and key sequence.Profit is in this way, it is assumed that key DNA sequence dna length is 25bp, then each represents 1 and expression 0
Possible cipher key combinations are (DNA is by four kinds of different base compositions：A、C、T、G).If character string has 1000, then can
The cipher key combinations of energy will be that required computing capability and memory space are all greatly beyond the social limit of current mankind.
(2) DNA passwords have highly-parallel computing capability.As described in document [19-20], 1 gram of DNA molecular can store 108TB number
According to, and all DNA moleculars can all carry out parallel computation.Using this advantage, each in character string can be simultaneously parallel
Operation, drastically increases calculating speed.
Embodiment of above is merely to illustrate the present invention, rather than limitation of the present invention.Although with reference to embodiment to this hair
It is bright to be described in detail, it will be understood by those within the art that, to technical scheme carry out it is various combination,
Modification or equivalent, without departure from the spirit and scope of technical solution of the present invention, the right that all should cover in the present invention is wanted
Ask among scope.
Claims (5)
1. a kind of DNA self-assembled structures, it is characterised in that the DNA self-assembled structures include balloon-shaped structure, by DNA nano junctions
Structure is formed with chain Q by base pairing, and wherein DNA nanostructure is hybridized with chain BHQ chains by DNA AB and formed；Chain Q includes head end
Sequence Q1, end sequence Q2 and intermediate sequence Q3, chain Q intermediate sequence Q3 are modified by fluorescent base Cy3, head end sequence Q1 chains and AB
A part of sequence of chain is complementary, and end sequence Q2 and AB chains another part sequence are complementary, and the 3 ' ends of the BHQ are by fluorescent quenching
Base BHQ is marked, and it is completely complementary with AB middle-of-chains sequence.
2. a kind of symmetric encryption system, it is characterised in that the symmetric encryption system includes DNA described in claim 1 from group
Assembling structure, and including XOR operating system.
3. a kind of symmetric encryption method of symmetric encryption system according to claim 2, it is characterised in that including following step
Suddenly：
Step one：In xor operation, by plain text, ciphertext or fluorescence signal and key change into binary string, plaintext, ciphertext or
Fluorescence signal and key respectively with AB chain part regional complementarities；
Step 2：Encryption, the DNA self-assembled structures of structure encrypt the DNA of key and plaintext as initial computing module, with
Initial computing module carries out strand replacement reaction and implements logic XOR, ciphertext or fluorescence signal is obtained, so as to complete plaintext
DNA ciphering process；
Step 3：The DNA of decryption, decruption key and ciphertext or fluorescence signal, strand replacement reaction is carried out with DNA self-assembled structures
Implement logic XOR, so as to complete the DNA decrypting processes of ciphertext or fluorescence signal；
Wherein, the xor operation of each of plaintext is completed in single test tube.
4. method according to claim 3, it is characterised in that in encryption and decryption processes, the AB chains of DNA self-assembled structures
It is AB1 chains and AB2 chains respectively, AB1 chains are different with the specific recognition region of AB2 chains, and the DNA of encryption key and decruption key
Sequence is different.
5. method according to claim 3, it is characterised in that the encryption that xor operation realizes information, production are performed to plaintext
Raw fluorescence signal represents " 1 ", does not produce fluorescence signal and represents " 0 ", and the fluorescence signal of all connects together expression ciphertext, so
After send recipient to.
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| CN104734848A (en) * | 2015-03-02 | 2015-06-24 | 郑州轻工业学院 | Recombinant DNA technology based information encrypting and hiding method and application |
| EP3472351B1 (en) | 2016-06-15 | 2020-10-28 | Ludwig-Maximilians-Universität München | Single molecule detection or quantification using dna nanotechnology |
| CN107437266A (en) * | 2017-07-11 | 2017-12-05 | 大连大学 | Image encryption method based on chaos system Yu DNA chain displacement model |
| CN113539363B (en) * | 2021-07-06 | 2022-06-17 | 湖南科技大学 | DNA hybridization information storage encryption method based on probe blocking and unblocking |
| CN113539379B (en) * | 2021-07-17 | 2022-07-08 | 湖南科技大学 | DNA hybridization information storage encryption method based on adding and removing of coding strand hairpin structure |
| CN115860768B (en) * | 2023-02-16 | 2023-06-02 | 浙江天演维真网络科技股份有限公司 | Source tracing method and device based on blockchain and electronic equipment thereof |
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